HAPimLD is a method of QTL(Quantitative Trait Loci) detection developed by Boitard et al. (2006). It is an interval-mapping method designed for unrelated individuals with no family information. It is based on a maximum-likelihood calculation and makes use of linkage disequilibrium through a Wright-Fisher modelisation of the population evolution.
hapim.LD.add(hap.trans.pere, hap.trans.mere, perf, CD, map, position, temps.depart, perfectLD, marq.hap.left)
- character matrix (number of individuals x number of markers) which provides, for each individual, the haplotype transmitted by its father.
- character matrix (number of individuals x number of markers) which provides, for each individual, the haplotype transmitted by its mother.
- numeric vector of length=number of individuals which contains the performances of individuals.
- numeric vector of length=number of individuals which contains the CD of individuals. var(perf$_i$)=error variance/CD$^2_i$
- numeric vector of length=(number of markers-1) which contains the distance in Morgan between two consecutive markers on the chromosome.
- numeric vector which contains the distance in Morgan of test positions from the beginning of the chromosome (first marker).
- numeric value which provides a start value for the evolution time of the population.
- need to be equal to TRUE: linkage disequilibrium is complete between mutated haplotype and Q allele at time 0.
- (number of markers of the mutated haplotype)/2.
Individual information have to be ranged in the same order in hap.trans.mere, hap.trans.pere, perf, CD.
All distances are assumed to be Haldame's distance in Morgan.
The returned value is a data frame which contains 8 columns:
-Value of Likelihood Ratio Test (LRT)
-Mutated (i.e. associated to Q allele) haplotype
-Estimate of the error variance
-Estimate of the Q allele effect
-Estimate of the time of population evolution
-Estimate of the Q allele frequency at time t=0
-Estimate of the performance mean
Boitard et al. Linkage disequilibrium interval mapping of quantitative trait loci. BMC Genomics (2006) 7:54.
publication to be submitted: C. Cierco-Ayrolles, S. Dejean, A. Legarra, H. Gilbert, T. Druet, F. Ytournel, D. Estivals, N. Oumouhou and B. Mangin. Combining linkage analysis and linkage disequilibrium for QTL fine mapping in animal pedigrees.
data(data.test) map=data.test[] hap.trans.mere=data.test[] hap.trans.pere=data.test[] perf=data.test[] CD=data.test[] # In this example,marker positions are: 0, 0.010, 0.020, 0.030, 0.040, 0.050, 0.060, # 0.070, 0.080, 0.090. # We want to test the presence/absence of a QTL between 2 consecutive markers, so position=c(0.005,0.015,0.025,0.035,0.045,0.055,0.065,0.075,0.085) # we use a 2 markers-associated haplotype. marq.hap.left=1 # We assume an evolution of 50 generations. temps.depart=50 perfectLD=TRUE hapim.LD.add=hapim.LD.add(hap.trans.pere,hap.trans.mere,perf,CD,map,position, temps.depart,perfectLD,marq.hap.left) hapim.LD.add
Documentation reproduced from package HAPim, version 1.3. License: GPL